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67 results for “plastid DNA”
New insights into infrageneric relationships of Lonicera (Caprifoliaceae) as revealed by nuclear ribosomal DNA cistron data and plastid phylogenomics
<p>The discontinuous geographic distribution pattern of plants in the north temperate zone has been a focus of biogeographic research, especially concerning the mechanisms behind the formation of such a pattern and the spatial and temporal evolution of this intermittent distribution pattern. Hypotheses of boreotropical origin, land bridge migration, and out-of-Tibet have been proposed to explain the formation of the discontinuous distribution pattern. The distribution of <em>Lonicera</em> shows a typical Europe-Asia-North America discontinuous distribution, which makes for a good case study to investigate the above three hypotheses. In this study, we inferred the phylogeny based on plastid genomes and a nuclear data set with broad taxon sampling, covering 83 species representing two subgenera and four sections. Both nuclear and plastid phylogenetic analyses found section <em>Isika</em> polyphyletic, while sections <em>Nintooa</em>, <em>Isoxylosteum</em>, and <em>Coelxylosteum</em> were monophyletic in subgenus <em>Chamaecerasus</em>. Based on the nuclear and chloroplast phylogeny, we suggest transferring L. <em>maximowiczii</em> and L. <em>tangutica</em> into section <em>Nintooa</em>. Reconstruction of ancestral areas suggests that <em>Lonicera</em> originated in the Qinghai-Tibetan Plateau (QTP) and/or Asia, and subsequently dispersed to other regions. The aridification of the Asian interior may have facilitated the rapid radiation of <em>Lonicera</em> in the region. At the same time, the uplifts of the Tibetan Plateau appear to have triggered the spread and recent rapid diversification of the genus on the QTP and adjacent areas. Overall, our results deepen the understanding of the evolutionary diversification history of <em>Lonicera</em>.</p>
Data from: Extensive allopolyploidy in the neotropical genus Lachemilla (Rosaceae) revealed by PCR ‐based target enrichment of the nuclear ribosomal DNA cistron and plastid phylogenomics
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New insights into infrageneric relationships of Lonicera (Caprifoliaceae) as revealed by nuclear ribosomal DNA cistron data and plastid phylogenomics
Open the record for dataset details and reuse information.
Data from: Phylogenetic systematics of subtribe Spiranthinae (Orchidaceae: Orchidoideae: Cranichideae) based on nuclear and plastid DNA sequences of a nearly complete generic sample
Subtribe Spiranthinae is the most species-rich lineage of terrestrial Neotropical orchids, encompassing > 500 species and 40 genera. We conducted maximum parsimony and maximum likelihood phylogenetic analyses of DNA sequence data of plastid matK-trnK and trnL-trnF and nuclear ribosomal ITS sequences for 36 genera and 182 species of Spiranthinae plus appropriate outgroups. The results strongly support monophyly of Spiranthinae (minus Discyphus, Discyphinae and Galeottiella, Galeottiellinae) and five major lineages, namely monospecific Cotylolabium (sister to the remaining Spiranthinae) and the Eurystyles, Pelexia, Spiranthes and Stenorrhynchos clades. Eighteen of the 27 genera of Spiranthinae for which more than one species was included in our analyses are monophyletic. Paraphyly of large genera, such as Cyclopogon and Sarcoglottis, resulted from segregation of particular species or groups of species exhibiting minor modifications of structures directly involved in pollination (e.g. nectary, rostellum and viscidium). Conversely, polyphyly has resulted from convergent evolution of floral attributes in distantly related species (e.g. Mesadenus). Some of the morphological characters used traditionally for generic delimitation and in non-molecular cladistic analyses of Spiranthinae are discussed against the evolutionary framework set by our molecular trees, emphasizing putative synapomorphies and problems derived from inappropriate character coding or incorrect homology assessments. Our ancestral area analysis indicates that Spiranthinae originated in eastern South America, with subsequent migrations and secondary radiations in Mesoamerica and North America, plus a derived migration from the latter region to the Old World (Spiranthes).
Data from: Pleistocene climate change and phylogeographic structure of the Gymnocarpos przewalskii (Caryophyllaceae) in the northwest China: Evidence from plastid DNA, ITS sequences, and Microsatellite
Northwestern China has a wealth of endemic species, which has been hypothesized to be affected by the complex paleoclimatic and paleogeographic history during Quaternary. In this paper, we used Gymnocarpos przewalskii as a model to address the evolutionary history and current population genetic structure of species in northwestern China. We employed two chloroplast DNA fragments (rps16 and psbB‐psbI), one nuclear DNA fragment (ITS), and simple sequence repeat (SSRs) to investigate the spatial genetic pattern of G. przewalskii. High genetic diversity (cpDNA: hS = 0.330, hT = 0.866; ITS: hS = 0.458, hT = 0.872) was identified in almost all populations, and most of the population have private haplotypes. Moreover, multimodal mismatch distributions were observed and estimates of Tajima's D and Fu's FS tests did not identify significantly departures from neutrality, indicating that recent expansion of G. przewalskii was rejected. Thus, we inferred that G. przewalskii survived generally in northwestern China during the Pleistocene. All data together support the genotypes of G. przewalskii into three groups, consistent with their respective geographical distributions in the western regions—Tarim Basin, the central regions—Hami Basin and Hexi Corridor, and the eastern regions—Alxa Desert and Wulate Prairie. Divergence among most lineages of G. przewalskii occurred in the Pleistocene, and the range of potential distributions is associated with glacial cycles. We concluded that climate oscillation during Pleistocene significantly affected the distribution of the species.
Data from: Strong nuclear differentiation contrasts with widespread sharing of plastid DNA haplotypes across taxa in European purple saxifrages (Saxifraga sect. Porphyrion subsect. Oppositifoliae)
The purple saxifrages, Saxifraga sect. Porphyrion subsect. Oppositifoliae, comprise the closest relatives of the arctic-alpine model plant S. oppositifolia and have a centre of diversity in the central and southern European mountain ranges. A multitude of taxa has been described and taxonomic concepts vary among different treatments. Using amplified fragment length polymorphism (AFLP) fingerprinting we show that some taxa indeed form strongly supported genetic entities best recognized on the species level (S. biflora, S. blepharophylla, S. retusa, S. rudolphiana, S. speciosa), while others (S. murithiana, S. paradoxa) are not genetically divergent at all. Saxifraga oppositifolia s. s. is phylogenetically incoherent. Plastid DNA sequence data show very limited congruence with the predominantly nuclear-derived AFLPs. Several co-distributed taxa (S. biflora, S. blepharophylla, S. oppositifolia s. s., S. retusa) share the same set of haplotypes. In the widespread species S. oppositifolia and S. retusa, highly divergent haplotype lineages were discovered, which exhibit a geographic rather than taxonomic structure. Recent and ancient hybridization and/or lineage sorting are likely responsible for the strong incongruence between data derived from nuclear and plastid genomes. Hybridization, which is known to occur among almost all taxa of this group when growing in sympatry, seems, however, insufficient to break down species barriers.
FIGURE 5 in The fundamental karyotype and plastid DNA of Alstroemeria piperata (Liliales, Alstroemeriaceae), a species endemic to the Valparaíso Region, Chile
FIGURE 5. Phylogenetic relationships from analyses of three plastid markers (petA-psbJ, trnL-rpl32 and intron rpl16) of Alstroemeria piperata and other Chilean alstroemerias (Baeza et al. 2022). A. Network inferred with TCS. B. Maximum likelihood tree inferred from DNA sequences and indels. The branch lengths in B were modified for aesthetic reasons.
Microsatellite (13 loci) and plastid DNA haplotypes in a population of Antirrhinum charidemi
<p>Genotype matrix of 182 Antirrhinum charidemi individuals sampled in 2007-2009 in the Barranco del Dragoncillo Blanco population in Cabo de Gata, Almería, Spain. Genotypes are given for 13 microsatellite loci and also include 3 plastid DNA haplotypes. Details on loci and genotyping conditions can be found in Forrest et al. 2017, https://doi.org/10.1093/botlinnean/bow002. Each individual is geolocated. Additional information include its corolla colour, its ancestry score in four gene pools obtained in Bayesian genetic cluster analysis (STRUCTURE), and its assignment to geo-genetic subpopulations. Metadata are available in a separate tab in the submitted spreadsheet. The data are analysed in a paper expected to be published in AoB Plants in 2025, titled: "Fine-scale genetic differentiation in the bee-specialized Antirrhinum charidemi covaries more strongly with microenvironment than with corolla colour"</p>
Fig. 1 in Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences
Fig. 1 Phylogenetic tree for Ranunculus species based on internal transcribed spacer (ITS) sequences. a Consensus tree inferred from the six most parsimonious trees (CI=0.72; RI=0.93). Numbers above branches show bootstrap values (3,000 replicates). b Majority-rule consensus of
FIGURE 1 in A new circumscription of the Mediterranean genus Anacyclus (Anthemideae, Asteraceae) based on plastid and nuclear DNA markers
FIGURE 1. Consensus tree (50% majority-rule) from Bayesian inference of the combined ITS + psbA-trnH dataset. Posterior probability values (PP) are indicated along branches (values below 0.50 are not shown). Colours of branches indicate tribal classification of the taxa. Phylogenetic placement of Anacyclus core species (Western Mediterranean species, WM) and Eastern Mediterranean (EM) species is highlighted in grey.
FIGURES 31–36 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 31–36. Neidium vandusenense sp. nov. SEM, external view. Fig. 31. Whole valve. Fig. 32. Central valve with multiple longitudinal canals and transapical central area. Proximal raphe branches evenly hooked. Fig. 33. Apex valve face and mantle showing concave mantle wall, longitudinal canals reducing to one at the apex. Fig. 34. Valve face showing developed ridge along one side of the raphe (arrow) and scattered surface depressions along the axial area. Areolae recessed with a finger-like cribra. Fig. 35. Apex with 3 evident copulae. Copulae open bands with 2 rows of pores. Lacina extends to band base (arrow). Fig. 36. Central region showing a weak elevation of the longitudinal canal. Scale bars = 20 μm: Fig. 31; 10 μm: Figs 32, 33; 2 μm: Figs 34–36.
FIGURES 79–82 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 79–82. Neidium lavoieanum sp. nov. SEM, internal view. Fig. 79. Half valve showing valve outline. Fig. 80. Broken longitudinal canal with areoale and internal valve face areolae. Arrow indicates renilimbia. Fig. 81. Internal central nodule with a covering over the verminae along the margin. Helictoglossae separated and aligned. Fig. 82. Apex, showing longitudinal canal extending to the apex and an erect helictoglossa next to hyaline thickened apex. Scale bars = 10 μm: Fig. 79; 5 μm: Fig. 81; 3 μm: Figs 80, 82.
FIGURES 1–5 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 1–5. Neidium iridis (Fig. 1) and Neidium beatyi sp. nov. (Figs 2 (holotype), 3–5). Scale bar = 50 μm.
FIGURES 75–78 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 75–78. Neidium lavoieanum sp. nov. SEM, external view. Fig. 75. Half valve. Fig. 76. Surface areolae with no occlusions and axial area mid-way along the valve. Fig. 77. Elevated central area with elongated areolae along the margin and recurved proximal raphe endings. Fig. 78. Apex showing lacinia and longitudinal canals extending to the apex. Scale bars = 10 μm: Fig. 75; 3 μm: Figs 76–78.
FIGURES 56–61 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 56–61. Neidium collare sp. nov. SEM, external view. Fig. 56. Whole valve. Fig. 57. Central valve with longitudinal canal and transapical central area. Proximal raphe branches deflected. Fig. 58. Valve face mantle junction with epivalve, hypovalve and copula band. Fig. 59. Valve face with developed areolae. Areolae without finger-like cribra. Fig. 60. Apex with open bands of copulae. Copulae with 2 rows of pores. Lacinia weakly developed. Fig 61. Apex showing no apparent lacinia. Longitudinal canals extend to the tip of the apex. Scale bars = 30 μm: Fig. 56; 5 μm: Figs 57, 58, 60; 3 μm: Fig. 61; 2 μm: Fig. 59.
FIGURES 37–44 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 37–44. Neidium vandusenense sp. nov.SEM, internal view.Fig. 37. Central area with offset forming interconnected helictoglossae. Surface depressions (ghost striae) present in the central area. Figs 38, 39. Apex showing upright formation of the helictoglossae at the edge of the terminal nodule. Longitudinal canals blend in with areolae. Figs 40, 41. Margin of the valve showing multiple longitudinal canals. Open chambered formation (Fig. 41 (arrow), apical and transapical). Fig. 42. Renilimbia surround hymenae covered areolae (arrow). Figs 43, 44. Open copula band with 2 rows of poroids. Scale bars = 5 μm: Figs. 37, 38, 43; 2 μm: Figs 40, 41; 1 μm: Figs 42, 44.
FIGURES 6–12 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 6–12. Neidium beatyi sp. nov. SEM, external view. Fig. 6. Whole valve. Fig. 7. Central area raphe with silica ridges along each side. Figs 8, 10. Valve margin and mantle with multiple longitudinal canals. Copulae 2 rows of poroids. Fig 9, 12. Recessed areolae chambered and interconnected with finger-like cribra. Fig. 11. Apex showing arrow-like bifurcate lacinia. Copulae (3 evident) open bands with no evident poroids. Scale bars = 20 μm: Fig. 6; 10 μm: Fig. 11; 5 μm: Figs 7–10; 2 μm: Fig 12.
FIGURES 62–68 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 62–68. Neidium collare sp. nov. SEM, internal view. Fig. 62. Whole valve. Figs 63, 67. Recessed areolae and longitudinal canals at mid-valve and close to apex. Figs 65, 66. Central area with offset forming interconnected helictoglossae. Very weak surface depressions (ghost striae) present in the central area. Remnants of renilimbia present (arrows). Fig. 64. Apex showing an erect helictoglossa at terminal nodule and single longitudinal canal extending to the apex. Fig. 68. broken valve showing the canal. Scale bars: 20 μm: Fig. 62; 5 μm: Figs 64, 65; 3 μm: Figs 63, 66, 67; 1 μm: Figs 68.
FIGURES 83 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 83. RaxML phylogenic tree construction showing boostrap (BS) confidence levels using the gene rbcL for selected taxa within the genus Neidium.
FIGURES 13–18 in Novel Neidium Pfitzer species from western Canada based upon morphology and plastid DNA sequences
FIGURES 13–18. Neidium beatyi sp. nov. SEM internal view. Fig. 13. Central area with linear forming interconnected helictoglossae. Fig. 14. Apex with a curved forming helictoglossa at the edge of the terminal nodule. A single prominent longitudinal canal extends to the nodule. Figs 15, 17. Multiple longitudinal canals; at center canal similar (Fig. 15), towards apex one becomes more prominent (Fig. 17, arrow). Fig. 16. Renilimbia surround hymenae covered areolae (arrow). Fig. 18. Open chambered formation (apically and transapically) of the longitudinal canal. Scale bars = 10 μm: Fig. 14; 5 μm: Figs 13, 17; 2 μm: Fig. 15: 500 nm: Figs 16, 18.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.